Appetite regulation is primarily mediated by the hypothalamus, within which many neurotransmitters that regulate feeding are shared by the stress response circuitry. Stressors, especially those occur during critical periods of life, influence epigenetic programming and gene expression in the long-term. Therefore, the aim of this dissertation was to elucidate how hypothalamic mechanisms of appetite regulation correlate with the stress response and epigenetic modifications, using avian models and intracerebroventricular administration of various appetite-regulating factors. We first administered two methylation modifiers, S-adenosylmethionine (SAM), a methyl donor, and 5-azacytidine (AZA), a methylation inhibitor, to determine their effects on appetite. When measuring food intake immediately post-injection, SAM didn't affect fed or fasted chickens from a line selected for low bodyweight (LWS, individuals with anorexia), but suppressed feeding in fed and fasted broilers. In Japanese quail, SAM transiently induced satiety in fed but not fasted chicks. Intriguingly, AZA increased feeding in fasted LWS but decreased it in fed chicks. While it didn't affect either fed or fasted broilers, AZA induced satiety in both fed and fasted quail. These results suggests that SAM/AZA can directly affect appetite depending on genetics and nutritional state. The LWS chickens, when injected with SAM or AZA on day of hatch, didn't show increased feeding to the orexigenic stimulation of neuropeptide Y central injection on day 5 post-hatch. This suggests that epigenetic modifications occurred following SAM/AZA injection and affect appetite regulation that persisted. In other studies, we injected broilers with prostaglandin E2 (PGE2) or β-melanocyte-stimulating hormone (β-MSH) since their effects on appetite are unknown in meat-type chicks. We found that they both potently induced satiety, but the effective duration was longer in β-MSH-injected birds (up to 9 hours) than in PGE2-injected chicks (lasted for 1.5 hours). They both activated the paraventricular nucleus of the hypothalamus. The satiety induced by β-MSH mainly involved corticotropin-releasing factor and mesotocin, while the effect of PGE2 included ghrelin and brain-derived neurotropic factor. Nevertheless, all affected appetite-related factors have connections with the stress response. Thus, our results demonstrate that the hypothalamic mechanisms underlying anorexia induced by different neuroactive molecules involve the stress response and epigenetic modifications. / Doctor of Philosophy / Eating disorders (EDs) all involve abnormal eating behaviors and altered body weight. These aberrant conditions are associated with a change in metabolism and pose great risk to human health and animal production, and are generally characterized by two opposite outcomes, anorexia and obesity. Although affected by multiple systems within the body, appetite regulation is mainly controlled by the brain, especially the hypothalamus. Thus, it is important to understand the hypothalamic mechanisms underlying the regulation of eating behavior. In the hypothalamus, many neurotransmitters affect multiple pathways, including the stress response and those that regulate appetite. Additionally, stress, especially when occurring during early life, can influence behaviors later in life through inducing epigenetic modifications (changes to the packaging of the DNA nucleotide sequence) that alter gene expression. Therefore, the aim of this dissertation was to elucidate how hypothalamic mechanisms of appetite regulation correlate with the stress response and epigenetic modifications, using avian models. To focus on the effects within the brain, we directly injected various appetite regulating factors into the brain in each of the experiments. Previously, our group demonstrated that early-life cold exposure and delayed food supply changed DNA methylation and affected expression of appetite-related genes and food intake in a chicken line predisposed to anorexia. We herein injected chicks with one of two methylation modifiers, S-adenosylmethionine (SAM), a methyl donor, and 5-azacytidine (AZA), a methylation inhibitor, to evaluate their effects on feeding behavior. When food intake was measured immediately after injection, SAM did not affect food intake in either fed or fasted line chickens from a genetic line selected for low body weight (LWS, individuals with anorexia), but suppressed food intake in both fed and fasted broiler (meat-type chickens) chicks. In Japanese quail, however, SAM only transiently induced satiety in fed chicks but not in fasted ones. Intriguingly, AZA increased food intake in fasted LWS chicks but decreased it in fed chicks, but AZA had no effects on food consumption in either fed or fasted broilers. Additionally, AZA suppressed food intake in both fed and fasted quail. These results suggest that SAM and AZA affect appetite differently depending on genetic background and nutritional states. LWS chickens, when injected with SAM or AZA on day of hatch, did not eat more after being injected with the potent hunger factor, neuropeptide Y, at 5 days of age. This indicates that epigenetic modifications occurred following SAM/AZA injection and had persisting effects on appetite regulation. In the other two studies, we injected broiler chicks with prostaglandin E2 (PGE2), a fatty acid-based molecule, or β-melanocyte-stimulating hormone (β-MSH), a peptide. These two molecules have been reported to regulate feeding behavior in rodents and layer-type chickens, but effects are unknown in broilers. They both potently decreased food intake in broilers, but the effective duration was much longer in β-MSH-injected birds (up to 9 hours) than in PGE2-injected chicks (lasted for 1.5 hours). They both activated the paraventricular nucleus of the hypothalamus, while β-MSH also activated the arcuate nucleus and ventromedial nucleus. We further found that the anorexia induced by β-MSH involved corticotropin-releasing factor, mesotocin, and their receptors, while the effect of PGE2 was associated with a change in ghrelin and brain-derived neurotropic factor gene expression. Nevertheless, all of these affected factors have connections with the stress response. Thus, results indicate that the hypothalamic mechanisms underlying anorexia induced by different neuroactive molecules involve the stress response and epigenetic modifications.

Type 2 Diabetes Mellitus (T2DM), a metabolic disorder denoted by elevated blood glucose levels and insufficient insulin action, is growing in prevalence worldwide . Barriers to improving disease outcome resolve primarily around identifying and intervening during the preliminary stages of insulin resistance, a state clinically referred to as pre-diabetes. Emerging evidence suggests that mitochondrial dysfunction may underlie , and potentially precede, progressive insulin resistance, suggesting that biomarkers indicative of mitochondrial dysfunction could predict disease risk and status. In this study, we examined epigenetic modifications, in the form of DNA methylation, in the promoter region of peroxisome proliferator activated receptor gamma coactivator 1 alpha (PGC-1α), a known regulator of mitochondrial biogenesis. Following the initiation of a high fat diet, we observed significant genotypic (DNA methylation) and phenotypic (mitochondrial copy number) alterations in C57/BL6 rodent models. These changes preceded overt disease onset, as classified by clinically utilized indices, which included the homeostatic model assessment for insulin resistance (HOMA-IR), the homeostatic model assessment for β-cell dysfunction (HOMA- β), and the quantitative insulin-sensitivity check index (QUICKI). Our data indicate that methylation analysis may serve as an effective clinical parameter to use in conjunction with physiological criterion for the diagnosis of pre-diabetes and the assessment of T2DM disease risk, and adds to the growing body of work seeking to elucidate the role. / Doctor of Philosophy / High blood glucose, referred to as type 2 diabetes (T2DM), increases the risk for heart and kidney disease, blindness, stroke, and death. Efforts to prevent T2DM have centered primarily around behavioral interventions, which include increased physical activity and decreased caloric intake. Importantly, the interventions are most effective when implemented early on in disease progression. In this study, we sought to examine the effects of a high fat diet on the epigenetic profile of PGC-1α, a gene responsible for maintaining mitochondrial biogenesis. The mitochondria, the powerhouse of the cell, is responsible for maintaining the energy systems in the body. Therefore, we examined how increasing in caloric intake resulted in changes in the epigenetic profile of the PGC-1α promoter, and how these changes impacted mitochondrial number. Further, we sought to examine how hypermethylation of PGC-1α led to changes in gene and protein expression in the mitochondria. Results from our study indicate that DNA methylation changes preceded disease onset, as characterized by the homeostatic model assessment for insulin resistance (HOMA-IR), the homeostatic model assessment for β-cell dysfunction (HOMA- β), and the quantitative insulin-sensitivity check index (QUICKI). Our data indicate that methylation analysis may serve as diagnostic and risk assessment tool for pre-diabetes and T2DM in conjunction with physiological measures.

Hypothalamus and adipose tissue are essential central and peripheral sites regulating energy homeostasis. Disruption of energy homeostasis can lead to diseases like anorexia and obesity in humans and reduced productivity in animals. Therefore, integrating knowledge in hypothalamic appetite regulation and adipose tissue metabolism is essential to maintain homeostasis. The aim of this dissertation was to elucidate molecular and cellular mechanisms of energy homeostasis in birds. We determined adipose tissue physiological changes during the first two weeks post-hatch in chickens from lines selected for low (LWS) and high (HWS) body weight. LWS was more dependent on yolk and subcutaneous fat mobilization for growth from hatch to day 4 post-hatch, with hyperplasia-predominated replenishment of the reservoir. In contrast, HWS was more dependent on feed for growth and maintained depot mass through hyperplasia and hypertrophy. From day 4 to 14 post-hatch, compared to maintenance of depot weight and adipocyte size in LWS, HWS accumulated clavicular and abdominal fat with minimal lipolysis. There was greater expression of precursor and proliferation markers in LWS with more apoptotic cells in the abdominal stromal vascular fraction on day 14 post-hatch, suggesting that apoptosis contributed to lower adipogenic potential and lack of abdominal fat in LWS. Exposure to thermal and nutritional stressors at hatch impaired growth by reducing yolk utilization and lowering body weight, lean and fat masses in LWS. Stress exposure resulted in increased global DNA methylation and DNA methyltransferase activity in the arcuate nucleus of the hypothalamus in LWS. Moreover, there was decreased binding to methyl-CpG-binding domain protein 2 in the promoter of corticotropin-releasing factor (CRF) because of hypomethylation in one CpG site at its core binding site in stressed LWS, which explains the increased CRF expression in the paraventricular nucleus of the hypothalamus. We next determined effects of nutritional status on adipose tissue physiology in Japanese quail, a less-intensively selected avian species. Six-hour fasting promoted lipolysis and gene expression changes in 7-day old quail with some changes restored to original levels within 1 hour of refeeding. Overall, our results reveal novel cellular and molecular mechanisms regulating appetite and adiposity in birds early post-hatch. / Doctor of Philosophy / Hypothalamus and adipose tissue are essential for regulating energy homeostasis in central and peripheral body sites, respectively. Disruption of energy homeostasis can lead to diseases like anorexia and obesity in humans and reduced productivity in animals. Therefore, integrating knowledge in hypothalamic appetite regulation and adipose tissue metabolism is essential to maintain energy homeostasis in both humans and animals. The aim of this dissertation was to elucidate molecular and cellular mechanisms of energy homeostasis in birds. We first determined adipose tissue physiological changes in chickens during the first two weeks post-hatch from lines selected for low (LWS) and high (HWS) body weight. These chickens have been selected for juvenile body weight for over 60 generations. The LWS are lean and anorexic, while HWS eat compulsively and develop obesity and metabolic syndrome. Such characteristics make the body weight line chickens good animal models to study physiological changes under anorexia and obesity. We found that LWS was more dependent on yolk reserves and subcutaneous fat mobilization for growth from hatch to day 4 post-hatch, with replenishment of the fat reservoir by increases in cell number. By contrast, HWS was more dependent on feed for growth and maintained depot mass through increased cell number and cell size. From day 4 to 14 post-hatch, HWS accumulated fat throughout the body, with less fat breakdown as compared to LWS. There was greater expression of cellular precursor and proliferation markers in LWS, with more dying cells in their abdominal fat on day 14 post-hatch, suggesting that programmed cell death is responsible for the lack of fat cell development in LWS. Exposure to thermal and nutritional stressors at hatch impaired growth by reducing yolk utilization and lowering body weight, lean and fat masses in LWS. There were many molecular changes in the hypothalamus, including changes in DNA that led to increased activation of corticotropin-releasing factor (CRF), a signaling molecule that is known to regulate the body's stress and appetite responses. Stress exposure increased global DNA methylation and DNA methyltransferase activity in the arcuate nucleus of the hypothalamus in LWS. Moreover, there was less methylation at the core binding site of methyl-CpG-binding domain protein 2 (MBD2), a protein that binds to methylated DNA to repress gene expression, in the CRF gene, in stressed LWS. In response to stress, there was decreased binding of MBD2 to the promoter region of CRF, which may explain increased expression of CRF in the paraventricular nucleus of LWS. These results demonstrate that early-life stressful events can cause epigenetic changes (like DNA methylation) that lead to alterations in physiology and behavior that persist to later in life. We next determined effects of nutritional status on adipose tissue physiology in Japanese quail, which have undergone less artificial selection than chickens and are more representative of a wilder-type bird. Six-hour fasting promoted lipolysis and gene expression changes in 7-day old quail with some changes restored to original levels within 1 hour of refeeding. Overall, our results provide novel perspectives on cellular and molecular mechanisms regulating appetite and adiposity in birds during early post-hatch development.

DNA methylation is one of the principal epigenetic modifications that plays an essential role in transcriptional regulation. After fertilization, mammalian embryos undergo dynamic changes in genome-wide DNA methylation patterns and the changes are essential for normal embryo development. Ten-eleven translocation (TET) methylcytosine dioxygenases are implicated in DNA demethylation by catalyzing the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). The three members of TET protein family, TET1, TET2, and TET3, are highly expressed in preimplantation embryos in a stage-specific manner. Previous studies demonstrated that TET proteins are involved in diverse biological processes such as gene regulation, pluripotency maintenance, and cell differentiation by mediating 5mC oxidation. My dissertation research was conducted to elucidate the mechanistic roles of TET proteins in epigenetic reprogramming of mammalian embryos using porcine embryos as a model. The first set of studies focused on the relationship between TET proteins and pluripotency. To understand the role of TET proteins in establishing pluripotency in preimplantation embryos, CRISPR/Cas9 technology and TET-specific inhibitors were applied. TET1 depletion unexpectedly resulted in an increased expression of NANOG and ESRRB genes in blastocysts, although the DNA methylation levels of NANOG promoter were not changed. Interestingly, transcript abundance of TET3 was increased in blastocysts carrying inactivated TET1, which might have had an effect on the increase of NANOG and ESRRB. When the activity of TET enzymes was inhibited to eliminate the compensatory increase of TET3 under the absence of functional TET1, the expression levels of NANOG and ESRRB were decreased and methylation level of NANOG promoter was increased. In addition, ICM specification was impaired by the inhibition of TET enzymes. These results suggest that the TET family is a critical component of the pluripotency network of porcine embryos by regulating expression of genes involved in pluripotency and early lineage specification. In the next set of studies, the presence of TET3 isoforms in porcine oocytes and cumulus cells was investigated to dissect the gene structure of TET3 that could assist in understanding mechanistic actions of TET3 in the DNA demethylation process. Among the three TET3 isoforms identified in cumulus cells, only the pTET3L isoform, which contains CXXC domain that carry DNA binding property, was verified in mature porcine oocytes. Expression level of the pTET3L isoform was much higher in mature oocytes compared to that in somatic cells and tissues. In addition, the transcript level of this isoform was significantly increased during oocyte maturation. These results suggest that pTET3L isoform is predominantly present in mature porcine oocytes and that CXXC domain may play an important role in DNA demethylation in zygotes. In a follow-up study, the role of the TET3 CXXC domain in controlling post-fertilization demethylation in porcine embryos was investigated by injecting TET3 GFP-CXXC into mature porcine oocytes. The injected CXXC was exclusively localized in the pronuclei, indicating that the CXXC domain may localize TET3 to the nucleus. The CXXC overexpression reduced the 5mC level in zygotes and enhanced the DNA demethylation of the NANOG promoter in 2-cell stage embryos. Furthermore, the transcript abundance of NANOG and ESRRB was increased in blastocysts derived from GFP-CXXC overexpressing zygotes. These results provide an evidence that the CXXC domain of TET3 is critical for post-fertilization demethylation of porcine embryos and proper expression of pluripotency related genes in blastocysts. In the last set of studies, the impact of MBD proteins on porcine embryo development was examined under the hypothesis that competitive binding of MBD and TET proteins to 5mC contributes to the proper maintenance of DNA methylation levels in embryos. Cloning of porcine MBD1, MBD3, and MBD4 from mature oocytes indicates that the genes are highly conserved among different species, implying the involvement of porcine MBD proteins in the maintenance of DNA methylation. MBD1 overexpression in oocytes impaired preimplantation development of porcine embryos, suggesting that the MBD1 overexpression may have negatively affected porcine embryo development because proper DNA methylation levels were not preserved under the high level of MBD1. Collectively, the studies in my dissertation demonstrate that TET family proteins are important epigenetic players involved in the regulation of pluripotency and reprogramming of DNA methylation, and are thus crucial for normal embryo development. The findings in the dissertation will improve our understanding of epigenetic events occurring in mammalian embryos, and have the potential to overcome epigenetic defects that are observed in pluripotent stem cells and in-vitro derived embryos. / Doctor of Philosophy / Epigenetic modifications are heritable changes affecting the level of gene expression without changing the sequence of the genome. DNA methylation, one of the biggest epigenetic marks in mammalian genome, is often correlated to gene repression. In mammals, DNA methylation patterns are dramatically changed during preimplantation development to acquire embryonic developmental potential. Understanding of the epigenetic changes occurring in preimplantation embryos is necessary for producing healthy domestic animals in agriculture and for developing strategies for the treatment of epigenetic defects in human. Ten-eleven translocation (TET) family enzymes, TET1, TET2, and TET3, are known to function as a DNA methylation modifier by converting 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). My dissertation research was performed to elucidate the role of TET family during preimplantation development using porcine embryos as a model. Pluripotency refers to the ability of cells to differentiate into all cell types of a mature organism. Pluripotent cells emerge in embryos as embryonic cells acquire lineage-specific characteristics. The first set of studies focused on the role of TET enzymes in regulating the pluripotency of porcine embryos. The impacts of inhibited activities of TET enzymes on the expression of pluripotency related genes were examined. We found that the inhibition of all TET enzymes leads to a decreased expression of pluripotency related genes, an altered DNA methylation level on a gene segment controlling pluripotency, and the impaired formation of pluripotent cell lineage in porcine embryos. This study demonstrates that the TET family is critical for the acquisition of pluripotency in porcine embryos. In the following sets of studies, the function of TET3 protein in the demethylation process occurring in preimplantation embryos was investigated. Fertilized mammalian embryos undergo genome-wide demethylation process to reset germ cell specific epigenetic marks into the embryonic epigenome. Previous studies indicate that TET3 is responsible for the demethylation process in mammalian embryos, although detailed mechanistic action of TET3 is still elusive. Here, we identified a predominant expression of a specific TET3 gene in porcine oocytes. The TET3 gene contained a CXXC domain, a potential DNA binding module, suggesting that TET3 may mediate DNA demethylation through its DNA binding property. To examine the function of the CXXC domain in TET3-mediated DNA demethylation, isolated CXXC domain was injected into porcine oocytes. The injection of CXXC domain facilitated DNA demethylation in embryos, demonstrating that the DNA binding property of TET3 is important for its functionality. In the last study, we investigated the importance of genes known to interact with TET enzymes in porcine embryos. Methyl-CpG-binding domain proteins (MBDs) have the ability to bind methylated region on the genome and play a critical role in mediating DNA methylation and gene repression. Our hypothesis was that a competitive binding of MBD and TET proteins to methylated regions was critical for proper DNA methylation levels in embryos. We identified that porcine MBD sequences were very similar to other species in terms of gene structure, indicating that the genes could also possess gene repressing activity by competing with TET enzymes during porcine embryo development. Injection of MBD1 mRNA to oocytes impaired normal embryo development, suggesting that the injected MBD1 may have negatively affected early embryo development in pigs by disrupting the proper maintenance of DNA methylation levels. My dissertation researches demonstrate that maintaining proper DNA methylation levels through the TET family is critical for normal embryo development in pigs. This research assists in improving our understating of epigenetic dynamics occurring in mammalian embryos and offers a potential solution to the epigenetic defects frequently observed in mammalian embryos produced through artificial reproductive technologies and pluripotent stem cells reprogrammed from somatic cells.

Excessive drinking during early pregnancy is associated with fetal developmental anomalies [1], particularly affecting heart formation, known as Congenital Heart Disease (CHD). This health concern is underscored by studies that indicate a high incidence of binge drinking among expectant mothers [1]. This research delves into alcohol's role in altering epigenetic patterns across the embryonic cardiac genome, seeking to isolate genes and their specific sites influenced by in utero alcohol exposure. The theory posits that ethanol-exposed embryonic mouse hearts will exhibit distinctive patterns of methylation in contrast to unexposed controls [2]. To investigate the proposed theory, ethanol was orally delivered to mouse models at a gestational stage critical for heart development, specifically embryonic day 9.5 (E9.5). Subsequently, at embryonic day 11.5 (E11.5)—a pivotal moment in cardiac morphogenesis—the mice were euthanized to harvest the embryonic hearts. The genomic material was then meticulously extracted from these hearts to enable a comprehensive analysis through whole-genome bisulfite sequencing (WGBS). Preliminary results revealed a marginal shift toward lower methylation levels without broad genomic changes in the ethanol treated samples [7]. Nonetheless, particular genes, like WNT7A gene, have been pinpointed for their suppressed activity following alcohol exposure, guiding further inquiries into aimed methylation changes and epigenetic variations that may illuminate the mechanisms by which maternal alcohol consumption prompts cardiac anomalies in CHD [7]

La réplication de l'ADN au cours de la phase S est initiée au niveau de sites spécifiques, appelés origines de réplication, qui sont distribués de manière adéquate le long des chromosomes et actifs une seule fois par cycle cellulaire. Les mécanismes qui contrôlent la position des origines de réplication restent énigmatiques chez les mammifères. Les travaux réalisés pendant cette thèse révèlent que la lysine méthyltransférase PR-Set7 humaine, responsable de la mono-méthylation de la lysine 20 de l'histone H4, induit un réarrangement chromatinien au niveau des nombreuses origines de réplication des gènes actifs. Celui-ci est caractérisé par la mono- et tri-méthylation de la lysine 20 de l'histone H4 et la tri-méthylation de la lysine 4 de l'histone H3. Ce profil de méthylation d'histones constituerait un signal épigénétique pour le recrutement sur la chromatine des facteurs nécessaires à la formation des origines de réplication, indépendamment d'un rôle sur la transcription. En effet, la présence d'une forme active de PR-Set7 en amont d'un gène rapporteur est suffisante pour induire cette cascade de méthylation et la formation d'une nouvelle origine de réplication au niveau de ce gène sans en modifier son expression. De la même manière, l'inactivation de l'enzyme dans une cellule conduit à l'inverse à une diminution du nombre total d'origines sans un effet majeur sur l'expression des gènes. Lors de la phase S, PR-Set7 est dégradée via le complexe E3 ligase CRL4Cdt2 et la protéine PCNA. Cette dégradation permet la disparition au niveau de la chromatine du signal de formation des origines, s'assurant ainsi qu'elles sont actives une seule fois par cycle. La mutation du domaine d'interaction avec PCNA est suffisante en effet pour empêcher la dégradation de PR-Set7, entraînant alors la formation et activation répétées des origines pendant la phase S (phénotype de sur-réplication). Ces résultats établissent la cascade de méthylation initiée par PR-Set7 pendant la mitose comme le mécanisme épigénétique contrôlant la mise en place et l'activation d'au moins la moitié des origines de réplication chez les mammifères. / In order to ensure accurate inheritance of genetic information through cell proliferation, chromosomes must be precisely copied once and only once and then correctly distributed to daughter cells. Chromosome replication occurs during the S phase of the cell cycle and is initiated at discrete chromosomal sites called replication origins. However, the ability to activate replication origins occurs during mitosis of the previous cell cycle and continuing into early G1 phase. This crucial step, called DNA replication licensing, consists of the assembly of a multi-protein pre-Replicative Complex (pre-RC) onto origins, making them competent for replication. During S phase, pre-RC are inhibited by different ways, that ensures that origins are activated only once per cycle and prevents DNA rereplication (multiple initiations from the same origin). In metazoans, functional replication origins do not show defined DNA consensus sequences, thus evoking the involvement of chromatin determinants in the selection of these origins.During my thesis, I have discovered that that the onset of licensing in mammalian cells coincides with an increase in histone H4 Lysine 20 monomethylation (H4K20me1) at replication origins by the methyltransferase PR-Set7. By genome mapping of H4-20me1 signals during the cell cycle, we found that nearly half of origins that fire during S phase are associated with H4-K20me1 during mitosis, when the process of replication licensing is activated. This mitotic H4-K20me1 signature is highly significant for origins located near transcription start sites and promoters that are characterized by the presence of CpG islands and H3-K4me3 signals. Furthermore, tethering PR-Set7 methylase activity to an origin-free genomic locus is sufficient to promote a chromatin remodeling follow by a creation of a functional origin of replication and promotes replication initiation. PR-Set7 and H4K20me1 are cell-cycle regulated, with high levels during M and early G1 and very low in S phase. At the onset of S phase, PR-Set7 undergoes an ubiquitin-mediated proteolysis, which depends on its interaction with the sliding-clamp protein PCNA and involves the ubiquitin E3 ligase CRL4-Cdt2. Strikingly, expression of a PR-Set7 mutant insensitive to this degradation causes the maintenance of H4K20me1 and repeated DNA replication at origins. This photolytic regulation controls the initiation of replication origin.This suggests that a cascade of lysine methylation events, initiated by PR-Set7 during mitosis, would define the position of origins in open chromatin structures.

La mucoviscidose (CF) est causée par des mutations sur le gène CFTR codant pour une protéine indispensable au maintien de l'homéostasie des transports hydro-électrolytiques au sein de l'épithélium des organes cibles de la pathologie, dérivés de l'endoderme (poumon, pancréas, appareil reproducteur). Entre ces différents tissus et au cours du développement fœtal, l'expression du gène varie, particulièrement dans le tissu pulmonaire où une répression est observée à l'âge adulte.Ce travail propose dans une première partie la caractérisation des modifications épigénétiques associées à la régulation spatio-temporelle physiologique de l'expression du gène CFTR dans les tissus humains sains adultes et fœtaux. Les résultats obtenus soulignent le rôle important des modifications post-traductionnelles des histones dans la régulation in vivo. Nous avons notamment observé i) un équilibre fin entre marques d'ouverture (acétylation) et de fermeture (H3K27Me3) de la chromatine sur la région promotrice du gène CFTR et ii) l'acétylation significative de régions cis-régulatrices intragéniques.La deuxième partie de ce travail consiste en l'évaluation des effets du SAHA, un inhibiteur d'histones déacétylases (HDACi) dans un modèle ex vivo d'épithélium nasal de patients atteints de mucoviscidose. Les résultats montrent que le SAHA ne restaure pas l'adressage membranaire de la protéine CFTR en contexte pathologique mucoviscidose (mutation p.(Phe508del)) dans des cellules CF différenciées en épithélium ex vivo. De plus, le SAHA induit une modification du profil inflammatoire des épithélia et une dé-différenciation épithéliale dans le modèle ex vivo montrant que les mécanismes d'action de cette molécule sont multiples et réversibles.Ce travail souligne la nécessité d'analyser in vivo les mécanismes physiopathologiques impliqués dans la mucoviscidose et d'évaluer l'impact des molécules thérapeutiques sur les protéines endogènes dans un modèle d'épithélium différencié. / Cystic fibrosis (CF) is caused by mutations in the CFTR gene encoding for a protein essential to maintain the homeostasis of fluid and electrolyte transport in the epithelium of endoderm-derived organs (lung, pancreas, reproductive tract) that are affected in CF patients. CFTR expression greatly varies between these tissues and during fetal development, particularly in the lung where repression is observed in adulthood .In the first part of this work, we characterized epigenetic modifications associated with the spatio-temporal regulation of CFTR gene expression in healthy human adult and fetal tissues. Our results emphasize the important role of histone post-translational modifications in this regulation in vivo. Specifically, we observed i) a fine balance between active (acetylation) and repressive (H3K27Me3) marks in the promoter region and ii) significant acetylation in intragenic cis-regulatory regions.In the second part of this work, we evaluated the effects of SAHA, a histone deacetylase inhibitor (HDACi) in an ex vivo model of nasal epithelium of CF patients. Our results show that SAHA can not restore CFTR protein to the apical membrane in a p.(Phe508del)-CFTR context in ex vivo CF differentiated epithelial cells. In addition, SAHA induces a change in the inflammatory profile of epithelia and epithelial dedifferentiation in the ex vivo model showing that the mechanisms of action of this molecule are multiple and reversible.This work highlights the need to analyze in vivo the pathophysiological mechanisms involved in Cystic Fibrosis and to evaluate the impact of therapeutic molecules on the endogenous proteins in a differentiated epithelium model.

A Doença de Parkinson é a segunda doença neurodegenerativa mais comum na atualidade. Cerca de 10% dos casos da doença estão relacionados com fatores genéticos e os outros 90% são devido a fatores ambientais e epigenéticos. Evidências indicam alterações na metilação de genes relacionados ao desenvolvimento da doença de Parkinson. No entanto, não se sabe o efeito de inibidores da metilação de DNA sobre a neurotoxicidade induzida por MPP+, uma neurotoxina que mimetiza processos neurodegenerativos associados ao Parkinson in vitro. Portanto, este trabalho teve como objetivo avaliar o efeito dos inibidores da metilação de DNA (RG108, n-ftaloil-l-triptofano e 5azadC, 5-aza-2´-deoxycytidina) e do doador universal de grupamentos metil (SAM, S-adenosilmetionina) sobre neurotoxicidade induzida por MPP+ em cultura de células imortalizadas (PC12), por meio da análise da viabilidade celular avaliada no teste do MTT (3 - [4,5 dimetiltiazol-2-il] -2,5-difenil-tetrazólio); e da análise de neuritogênese, na presença e na ausência de MPP+. Os resultados demonstraram que: 1. o tratamento com DNMTi (inibidor da DNA metiltransferase) ou com SAM induziram efeito per se sobre a viabilidade celular, apenas quando incubados em altas concentrações e em perídos prolongados (24h); 2. não modificaram a morte celular induzida pelo MPP+, em baixas concentrações, mas agravaram a neurotoxicidade quando incubados em altas concentrações ou por períodos prolongados (24h); 3. essas drogas induziram neuritogênese per se e potencializaram a neuritogênese induzida pelo NGF (fator de crescimento neural); 4. protegeram parcialmente contra a diminuição da neuritogênse induzida pelo MPP+. O conjunto de dados sugere que tanto os DNMTi quanto o SAM podem ser citotóxicos, dependen de suas concentrações e do tempo de exposição à droga. No entanto, essas drogas são capazes de aumentar a neuritogênese (diferenciação celular) e proteger contra a neurotoxicidade celular induzida pelo NGF, em células diferenciadas. / Parkinson\'s disease is the second most common neurodegenerative disease nowadays. About 10% of the disease cases are related to genetic factors and the other 90% are due to environmental and epigenetic factors. Evidence indicates changes in DNA methylation in genes related to the development of Parkinson\'s disease. However, the effect of DNA methylation inhibitors on MPP+-induced neurotoxicity, a drug that mimics neurodegenerative processes associated with Parkinson\'s in vitro, is not known. The aim of this study was to evaluate the effect of DNA methylation inhibitors (RG108, N-phthalyl-L-tryptophan and 5azadC, 5-aza-2?-deoxycytidine) and of the universal donor of methyl group (SAM, S-adenosyl methionine) on: 1. MPP+ -induced neurotoxicity in culture of immortalized cells (PC12), by analysis of cell viability in the MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium) test; 2. neuritogenesis, in the presence and absence of MPP +. Results indicated that: 1. treatment with DNMTi or SAM induced effects per se on cell viability only at higher concentrations and after prolonged periods of incubation (24h); 2. DNMTi (DNA methyltransferase inhibitors) and SAM increased cell differentiation and neuritogenesis per se, especially when incubated for 30 minutes, as well as they potentiated NGF-induced neurogenesis; 3. the drugs attenuated MPP+-induced effects on neuritogenesis. Altogether, these data suggests short treatment with both DNMTi and SAM do not cause cellular cytotoxicity (cell death), but are able to increase neuritogenesis (cell differentiation) and protect against MPP+-induced neurotoxicity in differentiated cells.

Les techniques de micromanipulation de molécules d’ADN uniques offrent des perspectives nouvelles pour lire et exploiter l’information contenue dans les génomes. Cela inclut le séquençage, la cartographie, le dénombrement de molécules et l'identification de modifications chimiques de l'ADN. Dans ce contexte, l'Équipe ABCDLab de l'ENS a développé une méthode utilisant l’ouverture et la fermeture mécanique répétée d’une molécule d’ADN en épingle à cheveux par pince magnétique. Cet outil permet de déterminer la position d'hybridation de petits oligonucléotides ainsi que celle d'anticorps révélant la position de marques épigénétiques. Un avantage de cette approche est de pouvoir travailler sur la même molécule pour d’une part identifier les marques épigénétiques et d'autre part réaliser une cartographie de sa position dans le génome. Mon travail de thèse consiste à développer un ensemble de méthodes bio-informatique visant à réaliser cette étape de cartographie. Le signal expérimental consiste en lecture des positions d’hybridation d’un, ou de plusieurs petits oligonucléotides sur la molécule étudiée. Cette mesure permet de construire une signature spécifique de la molécule que l’on peut rechercher dans le génome d’origine. Dans ce travail de thèse, j'ai réalisé des expériences avec sur pinces magnétiques pour acquérir des signatures moléculaires sur des molécules sélectionnées en aveugle dans E. coli. J'ai développé un logiciel capable de faire la recherche de ces signatures dans un génome et ensuite effectué l’ensemble du traitement des données pour tester le logiciel. Après plusieurs étapes d’optimisation, j’ai pu retrouver la position génomique des molécules étudiées, établissant ainsi une preuve de concept de cette stratégie de cartographie. Le travail a concerné l'ensemble de la chaîne de mesure : (1) le choix des sondes utilisées pour constituer la signature d’une molécule observée en optimisant un ensemble de critères liés aux conditions expérimentales et à la combinatoire des motifs de séquence. (2) la mise au point d’algorithmes de cartographie adaptés aux caractéristiques expérimentales des mesures. Enfin, j'ai testé ces algorithmes, à la fois sur des données simulées in silico et in vitro sur de l'ADN d'origine bactérienne. Je discuterais en quoi les performances des solutions de cartographie développées ici sont influencées par, d’une part les limites du montage expérimental actuel, et d’autre part les limites des approches bioinformatiques. Je présenterais les voies d’amélioration possibles de ces dernières. Mes travaux établissent qu'identifier des molécules d’ADN uniques par pinces magnétiques est possible dans le contexte d’application épigénétique et en génomique. / Single molecule micromanipulations technic offer new perspectives to read and unravel genome information. This includes sequencing, mapping, molecule counting and identification of DNA modifications. In this respect, ABCDLab team has developed a cutting edge method using repeated mechanical opening and closing of a DNA molecule with a hairpin shape using magnetic tweezers. This tool allows measuring along the DNA molecule the hybridization positions of oligonucleotides a few bases long and also to locate specific antibodies transiently bound to epigenetic markers. With this approach we can identify with the single molecule level epigenetics markers and localized them on the genome. My PhD work consisted of developing a set of bioinformatics methods to perform DNA mapping using magnetics tweezer signal consisting of hybridization positions along the studied molecule. This measurement may be viewed as a fingerprint of the molecule which can be searched on the reference genome. During my thesis, I have realized an experimental test using magnetic tweezers to acquire a set fingerprint data on a set of blinded selected molecules in the E. coli genome. I have developed a software performing a rapid search of these fingerprints inside the genome. Then I have performed the whole data treatment to check the software on the selected molecules. After several rounds of optimization, I have recovered the genetic position of the studied molecules, establishing a proof of concept of this cartography strategy. The work has addressed the whole measuring chain; (1) by choosing the oligonucleotides best adapted to obtain the molecular signature by optimizing the set of experimental constrains and combinatorial motifs of the sequence. (2) by tuning the cartography algorithm to adapt to the experimental measurement constrains. Finally, I have tested these algorithms, both on simulated data in silico and on experimental fingerprint in vitro. I shall discuss how the performances of these cartography solutions that have been developed here are impacted by the experimental limitations of the present technique, and by the bioinformatics limits. I shall present possible improvements to these methods. My studies constitute a proof of concept for genomic and epigenetic applications.

It was previously demonstrated that miR-199a was down-regulated in testicular germ cell tumor (TGCT) partly caused by hypermethylation of its promoter. More detailed analyses showed that miR-199a-5p, one of its two derivatives, suppressed TGCT invasiveness and proliferation via directing targeting PODXL and MAFB. The biological role of the other derivative, miR-199a-3p in TGCT, remains largely uncharacterized. In this project we identified DNMT3A, the de novo methyltransferase, as a direct target of miR-199a-3p using a 3’-UTR reporter assay. In NT2 (NTera 2) and HT (Hs 1.Tes) cells, miR-199a-3p regulated the expression of endogenous DNMT3A (both DNMT3A1 and DNMT3A2 isoforms), especially DNMT3A2 isoform. In clinical samples, the expression of DNMT3A2 and miR-199a-3p were reciprocally regulated. However, DNMT3A did not regulate miR-199a expression. Further characterization of miR-199a-3p revealed that it negatively regulated DNA methylation partly through targeting DNMT3A. MiR-199a-3p could restore the expression of APC and MGMT via de-methylation in their promoters. Our studies demonstrated the dysregulation of miR-199a-3p in TGCT may provide novel mechanistic insights into TGCT carcinogenesis and suggested a potential therapeutic use of synthetic miR-199a-3p oligonucleotides as effective demethylation agent in the treatment of TGCT. However, since DNMT3A expression did not regulate miR-199a expression, the mechanism of promoter DNA hypermethylation of miR-199a in TGCT needs further investigation. / MiR-199a is encoded by two loci in the human genome, namely, miR-199a-1 on chromosome 19 and miR-199a-2 on chromosome 1. Another microRNA, miR-214, also locates on chromosome 1. Previous study revealed that it is co-transcribed with miR-199a-2, which is directed by miR-199a-2 promoter. However, the biological significance of the co-expression of miR-199a and miR-214 remains largely unknown. In this project, it was determined that miR-199a and miR-214 were concordantly expressed in TGCT. Silencing of DNMT1 increased the expression of miR-199a and miR-214, accompanied by de-methylation in the promoters of miR-199a-1/2. Overexpression of TP53 down-regulated the expression of DNMT1 and increased the expression of mature miR-199-3p/5p and miR-214. In addition, silencing of PSMD10 up-regulated the expression of TP53, while miR-214 over-expression resulted in PSMD10 down-regulation and TP53 up-regulation. Collectively, our findings highlighted a miR-199a/miR-214/PSMD10/TP53/DNMT1 self-regulatory network, which caused the down-regulation of miR-199a, miR-214 and TP53, as well as the up-regulation of DNMT1 and PSMD10 in TGCT. These observations partly explain the mechanism of promoter DNA hypermethylation in miR-199a in TGCT. They also suggest a potential therapeutic approach by targeting the miR-199a/miR-214/PSMD10/TP53/DNMT1 regulatory network in the treatment of TGCT. / 先前的研究證實miR-199a在睾丸生殖細胞腫瘤 (簡稱睾丸癌) 中是低表達的，部分歸因於其啟動子區域過度甲基化。對其功能研究發現miR-199a能抑制睾丸癌細胞的生長，侵襲和轉移，且miR-199a的抑癌屬性應歸功於它的兩個衍生物之一miR-199a-5p。然而，miR-199a的另一個衍生物miR-199a-3p在睾丸癌中的生物學功能仍然在很大程度上是未知的。此研究中，DNMT3A被鑒定為miR-199a-3p的直接靶定目標。在NT2和HT細胞中，miR-199a-3p能調控內源性DNMT3A(DNMT3A1和DNMT3A2)的表達水準，尤其是DNMT3A2。在臨床樣本中，DNMT3A2的表達水準與miR-199a-3p的表達水準呈負相關。但DNMT3A並不能調控miR-199a的表達水準。進一步研究顯示過表達miR-199a-3p能減少APC和MGMT啟動子區域甲基化而恢復其表達水準。研究證實異常表達的miR-199-3p可能在睾丸癌的癌變過程中發揮作用，並提出一個潛在的治療方案，即使用miR-199a -3p作為有效的去甲基化藥劑治療睾丸癌。然而睾丸癌中導致miR-199a啟動子區域過度甲基化的機制有待進一步研究。 / 在人類基因組中，miR-199a-1(位於19號染色體)和miR-199a-2(位於1號染色體)都編碼miR-199a。同時miR -214也位於1號染色體，研究表明miR-214與miR-199a-2由miR-199a-2啟動子介導共同轉錄，但miR-199a和miR- 214共同表達的生物學意義仍未知。此研究中，miR-199a和miR-214在睾丸癌中的表達呈現一致性。沉默DNMT1後miR-199a和miR-214的表達水準顯著提高，並伴隨著miR-199a-1/2啟動子區域的DNA去甲基化。在NT2細胞中。過表達TP53能下調DNMT1的表達水準，同時上調miR-199-3p/5p和miR- 214的表達水準。此外，過表達miR -214能導致PSMD10表達水準的下調以及TP53表達水準的上調。綜上所述，我們提出一個miR-199a/miR-214/PSMD10/TP53/DNMT1自我調控網路，此調控通路能引起睾丸癌中miR-199a，miR-214和TP53表達水準的下調，以及DNMT1和PSMD10表達水準的上調，且部分解釋睾丸癌中miR-199a啟動子區域過度甲基化的機制，同時該調控網路可作為治療睾丸癌的一個潛在靶點。 / Chen, Bifeng. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2014. / Includes bibliographical references (leaves 103-127). / Abstracts also in Chinese. / Title from PDF title page (viewed on 20, December, 2016). / Detailed summary in vernacular field only. / Detailed summary in vernacular field only.